Fourier-transform infrared spectroscopic studies on avidin secondary structure and complexation with biotin and biotin-lipid assemblies

Biotin-phenosafranin as a new photosensitive conjugate for targeted therapy and imaging

A biotinylated phenazine compound as a phenosafranin conjugate (Biot-PSF) was synthesized and reported for the first time.

PRESENTATION OF BIOACTIVE EPITOPES WITH FREE N-TERMINI ON SELF-ASSEMBLING PEPTIDE NANOFIBERS

Branched self-assembling peptides bearing epitopes with free N-termini were designed. A lysine residue was used as branch point to present more than one epitopes in a single peptide. Atomic force microscope, circular dichroism and Fourier transform infrared spectroscopy data indicate that the N-terminus attached epitope sequences do not prevent the formation of the β-sheets and the self-assembling of these peptides into stable nanofibers in aqueous solutions. Rheology experiments show that these peptides could form self-supporting scaffolds once electrostatic repulsions were screened by electrolytes. Fluorescence spectra measurements upon binding of FITC-avidin to surfaces of nanofibers were performed to investigate the effect of charged aspartic acid residues in RGD epitopes at the lysine branching on packing and accessibility of the epitopes. Results show that the electrostatic interaction between hydrophilic side chains at branching and nanofiber surfaces may significantly affect the conformational freedom and accessibility of the epitopes at the periphery of the nanofibers. Cell entrapment experiments reveal that the attached RGD epitopes with free N-termini are biological active.

In situ IR spectroscopic studies of the avidin-biotin bioconjugation reaction on CdS particle films

Avidin-biotin bioconjugation reactions have been carried out on CdS nanoparticle films in H2O and D2O and investigated using in situ ATR-IR spectroscopic techniques. The experimental procedure involved the sequential adsorption of mercaptoacetic acid, the protein avidin, and the subsequent binding of the ligand biotin. The IR spectra of the solution-phase species mercaptoacetic acid, avidin, and biotin, at pH=7.2 were generally found to be similar in both H2O and D2O, with some minor peak shifts due to solvation changes. The IR spectra of the adsorbed species suggested that avidin may have undergone a conformational change upon adsorption to the CdS surface. In general, adsorption-induced conformational changes for avidin are likely, but to our knowledge have not been previously reported. The conformation of adsorbed avidin appeared to change again upon the binding of biotin, with the spectral data suggesting partial reversion to its native solution conformation.

Vibrational spectra and assignments using ab initio and density functional theory analysis on the structure of biotin

Density functional theory (DFT) and Hartree-Fock calculations were performed using the following models: HF/6-311G(d), B3LYP/6-311G(d), B3LYP/6-311+G(d) and B3PW91/6-311G(d) calculations were performed for biotin. It has been characterized by IR and X-ray. The calculated results show that the predicted geometry can well reproduce the structural parameters. Predicted vibrational frequencies have been assigned and compared with experimental IR spectra and they supported each other. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between Cp,m degrees, Sm degrees, Hm degrees and temperatures.

Conformational flexibility of avidin: the influence of biotin binding

Ligand binding to proteins is a key process in cell biochemistry. The interaction usually induces modifications in the unfolding thermodynamic parameters of the macromolecule due to the coupling of unfolding and binding equilibria. In addition, these modifications can be attended by changes in protein structure and/or conformational flexibility induced by ligand binding. In this work, we have explored the effect of biotin binding on conformation and dynamic properties of avidin by using infrared spectroscopy including kinetics of hydrogen/deuterium exchange. Our results, along with previously thermodynamic published data, indicate a clear correlation between thermostability and protein compactness. In addition, our results also help to interpret the thermodynamic binding parameters of the exceptionally stable biotin:AVD complex.

FTIR reveals structural differences between native beta-sheet proteins and amyloid fibrils

The presence of beta-sheets in the core of amyloid fibrils raised questions as to whether or not beta-sheet-containing proteins, such as transthyretin, are predisposed to form such fibrils. However, we show here that the molecular structure of amyloid fibrils differs more generally from the beta-sheets in native proteins. This difference is evident from the amide I region of the infrared spectrum and relates to the distribution of the phi/psi dihedral angles within the Ramachandran plot, the average number of strands per sheet, and possibly, the beta-sheet twist. These data imply that amyloid fibril formation from native beta-sheet proteins can involve a substantial structural reorganization.

UV resonance Raman study of streptavidin binding of biotin and 2-iminobiotin: comparison with avidin

UV resonance Raman (UVRR) spectroscopy is used to study the binding of biotin and 2-iminobiotin by streptavidin, and the results are compared to those previously obtained from the avidin-biotin complex and new data from the avidin-2-iminobiotin complex. UVRR difference spectroscopy using 244-nm excitation reveals changes to the tyrosine (Tyr) and tryptophan (Trp) residues of both proteins upon complex formation. Avidin has four Trp and only one Tyr residue, while streptavidin has eight Trp and six Tyr residues. The spectral changes observed in streptavidin upon the addition of biotin are similar to those observed for avidin. However, the intensity enhancements observed for the streptavidin Trp Raman bands are less than those observed with avidin. The changes observed in the streptavidin Tyr bands are similar to those observed for avidin and are assigned exclusively to the binding site Tyr 43 residue. The Trp and Tyr band changes are due to the exclusion of water and addition of biotin, resulting in a more hydrophobic environment for the binding site residues. The addition of 2-iminobiotin results in spectral changes to both the streptavidin and avidin Trp bands that are very similar to those observed upon the addition of biotin in each protein. The changes to the Tyr bands are very different than those observed with the addition of biotin, and similar spectral changes are observed in both streptavidin and avidin. This is attributable to hydrogen bond changes to the binding site Tyr residue in each protein, and the similar Tyr difference features in both proteins supports the exclusive assignment of the streptavidin Tyr difference features to the binding site Tyr 43.

Spin-label electron paramagnetic resonance studies on the interaction of avidin with dimyristoyl-phosphatidylglycerol membranes

The interaction of avidin--a basic protein from hen egg-white--with dimyristoyl-phosphatidylglycerol membranes was investigated by spin-label electron paramagnetic resonance spectroscopy. Phosphatidylcholines, bearing the nitroxide spin label at different positions along the sn-2 acyl chain of the lipid were used to investigate the effect of protein binding on the lipid chain-melting phase transition and acyl chain dynamics. Binding of the protein at saturating levels results in abolition of the chain-melting phase transition of the lipid and accompanying perturbation of the lipid acyl chain mobility. In the fluid phase region, the outer hyperfine splitting increases for all phosphatidylcholine spin-label positional isomers, indicating that the chain mobility is decreased by binding avidin. However, there was no evidence for direct interaction of the protein with the lipid acyl chains, clearly indicating that the protein does not penetrate the hydrophobic interior of the membrane. Selectivity experiments with different spin-labelled lipid probes indicate that avidin exhibits a preference for negatively charged lipid species, although all spin-labelled lipid species indirectly sense the protein binding. The interaction with negatively charged lipids is relevant to the use of avidin in applications such as the ultrastructural localization of biotinylated lipids in histochemical studies.

The X-ray three-dimensional structure of avidin

Avidin is a basic, highly stable, homotetrameric protein, isolated from bird egg-white, binding up to four molecules of D-biotin with extremely high affinity (Kd approximately 10(-15) M). The protein has been the object of different crystallographic investigations. In all the crystal structures, the four avidin subunits display almost exact 222 symmetry. Each avidin chain (128 amino acids) is arranged in a eight-stranded antiparallel beta-barrel, whose inner region defines the D-biotin binding site. The molecular bases of D-biotin affinity can be recognised in a fairly rigid binding site, which is sterically complementary to the shape and polarity of the incoming vitamin, and is readily accessible in the apoprotein structure. Avidin displays remarkable structural and functional relationships to the acidic protein sretpavidin, isolated from Streptomyces avidinii.

Albumin-binding surfaces: synthesis and characterization

The nature of the proteinaceous film deposited on a biomaterial surface following implantation is a key determinant of the subsequent biological response. To achieve selectivity in the formation of this film, monoclonal antibodies have been coupled to a range of solid substrates using avidin-biotin technology. Antibody clones varied in their antigen-binding activity following insertion of biotin groups into lysine residues. Biotinylated antibodies coupled to solid substrates via an immobilized avidin bridge retained their biological activity. During immobilization of avidin a significant proportion of the protein molecules were passively adsorbed rather than covalently attached to the surface. This loosely bound material could be removed by stringent elution procedures which resulted in a surface density of 5.4 pmol avidin cm(-2). Although these conditions would be harsh enough to denature monoclonal antibodies, they did not destroy the biotin-binding activity of the residual surface-coupled avidin, enabling the subsequent immobilization of biotinylated antibodies. The two-step immobilization technique allowed the use of gentle protein modification procedures, reduced the risk of surface-induced denaturation and removed loosely bound material from the surface. The versatility of the technique encourages its application to a wide range of immobilization systems where retention of biological activity is a key requirement.

FTIR study of the thermal denaturation of alpha-actinin in its lipid-free and dioleoylphosphatidylglycerol-bound states and the central and N-terminal domains of alpha-actinin in D2O

Fourier transform infrared (FTIR) spectroscopy has been carried out to investigate the thermal denaturation of alpha-actinin and its complexes with dioleoylphosphatidylglycerol (DOPG) vesicles. The amide I regions in the deconvolved spectra of alpha-actinin in the lipid-free and DOPG-bound states are both consistent with predominantly alpha-helical secondary structure below the denaturation temperatures. Studies of the temperature dependence of the spectra revealed that for alpha-actinin alone the secondary structure was unaltered up to 40 degrees C. But, in the presence of DOPG vesicles, the thermal stability of the secondary structure of alpha-actinin increased to 55 degrees C. The thermal denaturation mechanisms of the lipid-free and DOPG-bound states of alpha-actinin also vary. The secondary structure of the lipid-free alpha-actinin changed to be predominantly unordered upon heating to 65 degrees C and above. Whereas, the original alpha-helical structure in the DOPG-bound alpha-actinin retained even at 70 degrees C, the highest temperature we examined. Analysis of the reduction in amide II intensities, which is due to peptide H-D exchange upon heating alpha-actinin in D2O, showed that partially unfolded states with increased solvent accessibility but substantial secondary structures could be observed from 35 to 40 degrees C only if DOPG vesicles were present. A so-called "protamine precipitation" method has been developed to purify the N-terminal domain of alpha-actinin by use of the fact that the central domain of alpha-actinin is negatively charged but the N-terminal domain is positively charged. Thermal denaturation of the central and N-terminal domains of alpha-actinin were then investigated with FTIR. The secondary structure of the N-terminal domain of alpha-actinin was found to be thermally sensitive below 35 degrees C, which is characterized as the increase of the alpha-helical structure at the expense of the random coil upon heating the N-terminal domain from 4 to 35 degrees C. The membrane-binding ability of the N-terminal domain of alpha-actinin was proposed in terms of the analysis of the local electrostatic properties of alpha-actinin and the assignment of the amide II bands in the FTIR spctra of alpha-actinin.